Reproducible Research Final Project
Covid-19 Automated Report
Didem Paloglu, 425160
Huseyin Can Minareci, 417121
1. INTRODUCTION
1.1. Aim of the Project
In this project, it is aimed to visualize the main insights about Covid-19 pandemic. Starting from ‘2020-01-01’ , pandemic data from all countries is recorded in the data set until ‘2021-05-05’. The data set is very useful and gives wide information about status of countries in pandemic period. There are information about cases, deaths, reproduction rates, intensive care unit (icu) patients, tests, positiveness rates, vaccinations etc. Moreover, there are also additional information giving basic demographic statistics and also health statistics about countries such as smoking status by gender, life expectancy, population and its distribution over 65+ and 70+ aged people.
The main objective is providing an automated report so that any one who wonder the situation about a country or in time period could select desired values and create the automatic report for that country/time line. The default country is selected as United States and the time period is selected to cover all records of the data set.
1.2. Information About Data Set
The dataset is extracted from Our World in Data and it can be downloaded from GitHub Covid-19 Repository. It contains 59 columns and 86,118 rows giving information about each region and country in the world. To give the main structure, the head of data set is provided below:
| iso_code | continent | location | date | total_cases | new_cases | new_cases_smoothed | total_deaths | new_deaths | new_deaths_smoothed | total_cases_per_million | new_cases_per_million | new_cases_smoothed_per_million | total_deaths_per_million | new_deaths_per_million | new_deaths_smoothed_per_million | reproduction_rate | icu_patients | icu_patients_per_million | hosp_patients | hosp_patients_per_million | weekly_icu_admissions | weekly_icu_admissions_per_million | weekly_hosp_admissions | weekly_hosp_admissions_per_million | new_tests | total_tests | total_tests_per_thousand | new_tests_per_thousand | new_tests_smoothed | new_tests_smoothed_per_thousand | positive_rate | tests_per_case | tests_units | total_vaccinations | people_vaccinated | people_fully_vaccinated | new_vaccinations | new_vaccinations_smoothed | total_vaccinations_per_hundred | people_vaccinated_per_hundred | people_fully_vaccinated_per_hundred | new_vaccinations_smoothed_per_million | stringency_index | population | population_density | median_age | aged_65_older | aged_70_older | gdp_per_capita | extreme_poverty | cardiovasc_death_rate | diabetes_prevalence | female_smokers | male_smokers | handwashing_facilities | hospital_beds_per_thousand | life_expectancy | human_development_index | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | AFG | Asia | Afghanistan | 2020-02-24 | 1 | 1 | NA | NA | NA | NA | 0.03 | 0.03 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 2 | AFG | Asia | Afghanistan | 2020-02-25 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 3 | AFG | Asia | Afghanistan | 2020-02-26 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 4 | AFG | Asia | Afghanistan | 2020-02-27 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 | |
| 5 | AFG | Asia | Afghanistan | 2020-02-28 | 1 | 0 | NA | NA | NA | NA | 0.03 | 0.00 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 8.33 | 38928341 | 54.42 | 18.6 | 2.58 | 1.34 | 1803.99 | NA | 597.03 | 9.59 | NA | NA | 37.75 | 0.5 | 64.83 | 0.51 |
Note 1: The default country for the report is chosen as United States. If the user of the report does not specify any country, the report will be created for United States.
Note 2: The default time period for the report is chosen to cover all time range (between 2020-01-01 and 2021-05-05). If the user of the report does not specify any time period, the report will be created for all time period.
1.3. General Situation of Covid-19 Pandemic in the World
Before starting detailed analysis, it is beneficial to provide distribution and density of total Covid cases for all countries to give the general idea/information about what’s happening in the world. In below map, total cases (from first reported case to last reported case) in all avaliable countries between 2020-01-01 and 2021-05-05 is provided. The wider bubbles indicates the higher number of cases in countries.
2. DETAILED ANALYSIS ABOUT COVID-19
In this section, several analysis about Covid-19 pandemic is provided. All analysis are reported for United States in the time interval 2020-01-01 and 2021-05-05. It should be noted that one can produce different report results for other countries and time interval by changing the country and dates in the “Knit with Parameters” option.
Before jumping detailed visual analysis, the key highlights about Covid-19 are provided. This highlights give the general characteristics of Covid-19 pandemic in United States .
General characteristics of COVID-19 in United States
Between 2020-01-01 and 2021-05-05, the number of total cases has been reach to 32557444 in United States. The maximum number of daily cases in this period has been reached to 300310, which is reported on 2021-04-28 and average daily case is 69419. In this period, 579275 people have died and maximum number of death is recorded as 4475 on 2021-01-20 and average daily death is 1341. Reproduction rate is 1.16, which is below from world average (world average=1.16). It means that, on average, every 10 people with Covid will infect 12 other people.
2.1. Total Cases and Daily Cases
In the following graph, the uptrend of the total cases and daily cases of Covid-19 is provided. The orange line represents the total trends and blue bars represent the daily cases. Insight about the cases for United States is as below:
The maximum daily case has been recorded as 300310 in 2021-01-02, between 2020-01-01 and 2021-05-05. In this period, total cases reached to 32557444.
2.2. Daily Cases and Deaths
The relation between cases and deaths is important insight about the pandemic. In the following graph, daily cases and dailys deaths between 2020-01-01 and 2021-05-05 is provided.
The maximum daily case has been recorded as 300310 in 2021-01-02, between 2020-01-01 and 2021-05-05. Moreover, the correlation between daily cases and daily deaths is 0.73, and it indicates that there is strong positive correlation between cases and deaths.
2.3. Daily Tests and Positive Rates
The following graph shows the Covid-19 test statistics and the positivity rates. The rates is provided with orange line and tests (total test and positive tests) are provided with bars.
The maximum total test number in a day is recorded as 2309954 in 2021-01-06, between 2020-01-01 and 2021-05-05. The total test numbers have been reached to 418273496 in this period. Among daily tests, the number of average positive test is 68392. The positivity rate is approximately 0.07 in this period. The highest positivity rate is 0.199, which is recorded in 2020-04-06.
2.4. COVID-19 Hospitalizations
In the following graph, the hospitalizations of people who suffer from Covid-19 is provided. There are two type of patients in the graph. Dark blue bars indicates the patients hospitalized and gold-coloured bars indicates the patients in intensive care units (ICU).
The total hospitalized patients is reached its maximum with 129637 people in 2021-01-06. Among these patients, 23.13 % of patients are in ICU.
2.5. COVID-19 Vaccinations
General characteristics of COVID-19 Vaccination in United States
United States, uses Johnson&Johnson, Moderna, Pfizer/BioNTech vaccines in order to fight with COVID-19.
Source: Centers for Disease Control and Prevention (https://covid.cdc.gov/covid-data-tracker/#vaccinations).
Between 2020-01-01 and 2021-05-05, the number of total vaccination has been reach to 249566820 in United States. While 148562891 amount of people got only 1st dose of vaccination, 107346533 people got both doses and got fully vaccinated. The maximum number of vaccination per day in this period has been reached to 4629928, which is reported on 2020-02-20 and average daily vaccination is 2097327.
1st dose vaccination rate is 45 %, which is above from world average (world average= 14 %). And fully vaccinated rate is 32 %, which is above from world average (world average= 6 %).
2.5.1. First Dose and Fully Vaccinated
In the following plot vaccinations in United States between 2020-01-01 and 2021-05-05 can be seen.
First day they started to vaccinate people in the United States was 2020-12-21. From that time until 2021-05-05 in total 148562891 person got at least 1 dose of vaccination while 107346533 people got fully vaccinated against covid. Maximum difference between at least 1st dose and fully vaccinated is 47324578 and it is 14.3 % of population which was seen on 2021-04-15. From other hand minimum difference is 8348671 and it is 2.5 % of population which happened on 2021-01-14. If it comes to average difference at least first dose and fully vaccination is 32550745 and it is 9.8 % of population which was around 2021-03-15.
2.5.2. COVID-19 Daily Vaccinations and Trend
In the following plot daily new vaccinations and trend in United States between 1st Day and 2021-05-05 can be seen.
If it comes to daily vaccination in the United States as we can see from the trend, it increases until 2021-04-05 and then decreases. Maximum new vaccination per day is 4629928 and it is 1.4 % of population which was seen on 2021-04-10. From other hand minimum new vaccination is 57909 and it is 5790900 % of population which happened on 2020-12-21. If it comes to average daily new vaccinations is 2097327 and it is 0.6 % of population which was around 2021-04-26.